Fix merge conflict.

composer.json

@@ -4,7 +4,9 @@
   },
   "require-dev": {
     "statonlab/tripal-test-suite": "1.5.*",
-    "phpunit/php-code-coverage": "^6.1"
+    "phpunit/php-code-coverage": "^6.1",
+    "squizlabs/php_codesniffer": "^2.9.1",
+    "drupal/coder": "^8.2"
   },
   "autoload": {
     "psr-4": {

docs/contributing.rst

@@ -13,3 +13,23 @@ It provides a database seeder to make development a bit easier. Once you've inst
 .. warning::
 
 	**NEVER** run seeders on production sites. They will insert fictitious data into Chado.
+
+Coding Standards
+------------------
+
+This project uses code climate to ensure coding standards are met. We suggest you use php_codesniffer locally to check coding standards before submitting a Pull Request for a smoother experience. This can be done as follows:
+
+1. Run ``composer up`` within the Tripal HQ directory. This will install php_codesniffer locally.
+2. Check coding standards by running ``./vendor/bin/phpcs --standard=vendor/drupal/coder/coder_sniffer/Drupal/ruleset.xml [file]`` where ``[file]`` contains your changes. This will output a report meant to help you improve your code.
+3. php_codesniffer includes a tool for automatically fixing many warnings you may have encountered. To run it execute ``./vendor/bin/phpcbf --standard=vendor/drupal/coder/coder_sniffer/Drupal/ruleset.xml [file]`` on the same file. Make sure to review any changes it makes.
+4. Manually fix any remaining errors and re-run step 2 to confirm.
+
+We truely appretiate your effort in keeping our project standards compliant!
+
+Automated Testing
+-------------------
+
+This project uses TripalTestSuite and phpunit for automated testing. To run tests:
+
+1. Run ``composer up`` within the Tripal HQ directory. This will install phpunit locally.
+2. Run ``.vendor/bin/phpunit`` to execute all tests.

docs/introduction.rst

@@ -9,12 +9,14 @@ What is Tripal HQ?
 
 Tripal HQ provides a user-contributed content control center and administrative toolbox for your Tripal site.  This means that users are able to create whatever Chado content you'd like them, but withhold inserting it into the database until someone has approved it.
 
+Tripal HQ Imports extends this functionality to data importers. In this way your users can submit any single-page Tripal importer and both the file and associated metadata will remain in holding for administrative review. Once approved, the importer will be run, inserting all data into the database.
+
 HQ also provides a Chado-specific permission (currently only supporting organisms).  If you have lots of organisms on your site, and want to allow users to be the admin of a specific organism or set of organisms, this feature is for you!
 
 Module Features
 ================
 
-* Users create data using your existing Bundle configuration- no extra forms!
+* Users create data using your existing Bundle configuration or Importers- no extra forms!
 * User dashboard area for viewing pending submissions
 * Admin dashboard for viewing submissions
 * Chado-based permissions to create admins for certain projects or organisms

docs/setup/install.rst

@@ -13,7 +13,7 @@ Clone the repo with github and enable the module with drush.  For example:
 
   cd /var/www/html/sites/all/modules/custom/
   git clone https://github.com/statonlab/tripal_hq.git
-  drush pm-enable tripal_hq tripal_hq_permissions
+  drush pm-enable tripal_hq tripal_hq_imports tripal_hq_permissions
 
 
 

docs/setup/permissions.rst

@@ -14,6 +14,7 @@ On installation, HQ defines the following permissions:
 * **Administer CHADO-specific Tripal HQ content**: Lets you specify what Chado content a user can administer.
 * **Create Tripal HQ content requests**: Allows users to submit content requests and view their dashboard.
 * **Propose Tripal HQ Content** permission for each of your defined bundles.  This will let you configure which bundles can be proposed by users.
+* **Propose Tripal HQ Data File** permission for each available Tripal Importer.  This will let you configure which importers can be proposed by users.
 
 To get started, you'll need to create a role for your content submitters, and give them the "Create Tripal Content Requests" permission, plus whatever specific bundle permissions you'd like them to see.
 

docs/usage.rst

@@ -5,6 +5,9 @@ Module Usage
 Users
 =======
 
+Content Pages
+---------------
+
 User content submission can be reached at ``tripal_hq/bio_data``.
 
 
@@ -14,6 +17,17 @@ Approved, pending, and rejected content is displayed in the table.  Clicking the
 
 Click the "Submit Content" button to submit Tripal Content.  The submission form is the **exact same form** as the admin content creation form.
 
+Data Files
+------------
+
+Data files can be submitted by users at ``tripal_hq/bio_data/import-data``.
+
+.. image:: /_static/img/imports_userdash.png
+
+As you can see in the above screenshot when Tripal HQ Imports is enabled, it adds a second table to the user dashboard. This makes it easy to see the status of both your content and data file submissions.
+
+To submit a new data file with associated metadata, click "Import data file". You can edit a pending submission by clicking the "Edit" link beside that particular data file. Both the submission add and edit forms match the administrative data import forms exactly which ensures consistent metadata and validation.
+
 Admins
 =======
 

tripal_hq_imports/includes/tripal_hq_imports.api.inc

@@ -53,6 +53,7 @@ function tripal_hq_get_importers() {
  *
  * @param string $class
  *   The TripalImporter class to include.
+ *
  * @return bool
  *   TRUE if the field type class file was found, FALSE otherwise.
  */
@@ -80,6 +81,7 @@ function tripal_hq_load_include_importer_class($class) {
  *
  * @param int $submission_id
  *   The id of the submission you would like returned.
+ *
  * @return object
  *   An object describing the submission.
  */
@@ -97,6 +99,7 @@ function tripal_hq_imports_get_submission_by_id($submission_id) {
  *
  * @param object $submission
  *   An object describing the submission to be rejected.
+ *
  * @return bool
  *   True if the rejection was successful, FALSE otherwise.
  */
@@ -124,6 +127,7 @@ function tripal_hq_imports_reject_submission($submission) {
  *
  * @param object $submission
  *   An object describing the submission to be approved.
+ *
  * @return bool
  *   Returns FALSE if an error is encountered, otherwise TRUE.
  */
@@ -165,10 +169,12 @@ function tripal_hq_imports_approve_submission($submission) {
  *   A form field defined using the Drupal Form API.
  * @param array $values
  *   The full values list for the form.
+ * @param string $element_key
+ *   THe key of the element to be checked.
  * @param string $op
  *   One of 'edit' or 'view' where the second will be read-only.
  */
-function tripal_hq_editview_form_field(&$form_field, $values, $element_key, $op) {
+function tripal_hq_editview_form_field(array &$form_field, array $values, $element_key, $op) {
 
   if (isset($form_field['#type']) and ($form_field['#type'] == 'fieldset')) {
     foreach (element_children($form_field) as $child_element) {